Not surprisingly, many more differentially expressed genes than differentially expressed proteins or phosphopeptides were quantified. Of the 2,108 mRNA transcripts, 390 proteins, and 345 phosphorylated proteins differentially expressed (FDR or p<0.05) that could be matched to gene names or UniProt accession numbers, 87 transcripts and proteins, 34 proteins and phosphorylated proteins, and 45 transcripts and phosphorylated proteins overlapped between the respective datasets (Figure 5A). Eight transcripts, proteins, and phosphorylated proteins were quantified as significantly expressed differentially between lines in all three datasets (Figure 5A; Supplementary Table 1). Of the overlapping 87 transcripts/proteins found in the RNA-sequencing and quantitative proteomics analysis, 68 exhibited coordinated regulation (both mRNA and protein were increased or both mRNA and protein were decreased) and 19 demonstrated divergent regulation (increased in one analysis, decreased in the other). For these 87 overlapping genes and proteins, there was a moderately strong relationship between mRNA transcript log2 FC and protein log2 AR (R-square = 0.334, p<0.0001; Figure 5B). When comparing shared GO enrichment across the networks of differentially expressed genes, proteins, and phosphorylated proteins described above, 26 BP, 3 MF,
